[phenixbb] reduce and ready_set problem

Jianghai Zhu jzhu at idi.harvard.edu
Wed Jan 6 12:52:11 PST 2010


I believe I have reported this bug before, but it is not fixed in the phenix.reduce and phenix.ready_set yet.  The problem is the hydrogens added by reduce when there is a glycan.  Here is the error message.

  Number of atoms with unknown nonbonded energy type symbols: 12
    "ATOM   8332 HD22 ASN B  99 .*.     H  "
    "ATOM  11820 HD22 ASN B 320 .*.     H  "
    "ATOM  12615 HD22 ASN B 371 .*.     H  "
    "ATOM  14058  HO4 NAG B3320 .*.     H  "
    "ATOM  14086  HO4 NAG B3321 .*.     H  "
    "ATOM  14136  HO4 NAG B3371 .*.     H  "
    "ATOM  22458 HD22 ASN D  99 .*.     H  "
    "ATOM  25955 HD22 ASN D 320 .*.     H  "
    "ATOM  26750 HD22 ASN D 371 .*.     H  "
    "ATOM  28256  HO4 NAG D3320 .*.     H  "
    ... (remaining 2 not shown)

Sorry: Fatal problems interpreting PDB file:
  Number of atoms with unknown nonbonded energy type symbols: 12
    Please edit the PDB file to resolve the problems and/or supply a
    CIF file with matching restraint definitions, along with
    apply_cif_modification and apply_cif_link parameter definitions
    if necessary.
    Also note that phenix.ready_set and phenix.elbow are available
    for creating restraint definitions (CIF files).

The hydrogen left on the N atom of the ASN is correct, but should be named as HD21 as defined in the ccp4 cif library.  And the HO4 for the NAG glycan is just wrong.  I have to delete all these hydrogens to get phenix.refine going. 

-- Jianghai

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